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This is the command insegt that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


insegt - INtersecting SEcond Generation sequencing daTa with annotation

SYNOPSIS

insegt [OPTIONS] <ALIGMENTS-FILE> <ANNOTATIONS-FILE>

DESCRIPTION

INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end)
by using gene-annotations.

Input to INSEGT is a SAM file containing the alignments and a file containing the
annotations of the reference genome, either in GFF or GTF format.

-h, --help

Displays this help message.

--version

Display version information

Options: :

-ro, --read-output FILE

Output filename for read-output, which contains the mapped annotations followed by
their parent annotation. Valid filetype is: gff.

-ao, --anno-output FILE

Output filename for anno-output, which contains the annotations similar to the GFF
input and additionally the counts of the mapped reads and the normalized expression
levels in RPKM. Valid filetype is: gff.

-to, --tuple-output FILE

Output filename for tuple-output, which contains exon tuples connected by reads or
matepairs. Valid filetype is: gff.

-fo, --fusion-output STR

Output filename for fusion-output, which contains exon tuple of gene fusions
(Advanced option, currently no output port for KNIME). One of gff.

-n, --ntuple INT

ntuple Default: 2.

-o, --offset-interval INT

Offset to short alignment-intervals for search. Default: 5.

-t, --threshold-gaps INT

Threshold for allowed gaps in alignment (not introns). Default: 5.

-c, --threshold-count INT

Threshold for min. count of tuple for output. Default: 1.

-r, --threshold-rpkm DOUBLE

Threshold for min. RPKM of tuple for output. Default: 0.0.

-m, --max-tuple

Create only maxTuple (which are spanned by the whole read).

-e, --exact-ntuple

Create only Tuple of exact length n. By default all tuple up to the given length
are computed (if -m is set, -e will be ignored).

-u, --unknown-orientation

Orientation of reads is unknown.

EXAMPLES

insegt
example/alignments.sam example/annotations.gff

Run INSEGT on example files with default parameters.

insegt -m example/alignments.sam example/annotations.gff

Run INSEGT on example files and only compute maxTuple.

insegt -c 2 example/alignments.sam example/annotations.gff

Run INSEGT on example files and only output tuple with a min. count of 2.

VERSION

insegt version: 1.0 Last update 2012-09-11

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